J. D. Badji´cbadji´c, V. Balzani, A. Credi, S. Silvi, and J. F. Stoddart, A Molecular Elevator, Science, vol.303, issue.5665, pp.1845-1849, 2004.
DOI : 10.1126/science.1094791

V. Balzani, A. Credi, and M. Venturi, Molecular devices and machines -Concepts and perspectives for the nano world, 2008.

M. Blinov, J. Faeder, B. Goldstein, and W. Hlavacek, BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics, vol.20, issue.17, p.3289, 2004.
DOI : 10.1093/bioinformatics/bth378

Y. Cao, H. Li, and L. Petzold, Efficient formulation of the stochastic simulation algorithm for chemically reacting systems, The Journal of Chemical Physics, vol.121, issue.9, pp.4059-4067, 2004.
DOI : 10.1063/1.1778376

L. Cardelli, Brane Calculi, Danos and Schächter [14], pp.257-278
DOI : 10.1016/S0020-0190(01)00214-9

F. Ciocchetta, A. Duguid, S. Gilmore, M. L. Guerriero, and J. Hillston, The Bio-PEPA Tool Suite, 2009 Sixth International Conference on the Quantitative Evaluation of Systems, pp.309-310, 2009.
DOI : 10.1109/QEST.2009.27

A. Credi, M. Garavelli, C. Laneve, S. Pradalier, S. Silvi et al., <mml:math altimg="si2.gif" display="inline" overflow="scroll" xmlns:xocs="http://www.elsevier.com/xml/xocs/dtd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.elsevier.com/xml/ja/dtd" xmlns:ja="http://www.elsevier.com/xml/ja/dtd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:tb="http://www.elsevier.com/xml/common/table/dtd" xmlns:sb="http://www.elsevier.com/xml/common/struct-bib/dtd" xmlns:ce="http://www.elsevier.com/xml/common/dtd" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cals="http://www.elsevier.com/xml/common/cals/dtd"><mml:mstyle mathvariant="monospace"><mml:mi>nano</mml:mi></mml:mstyle><mml:mi>??</mml:mi></mml:math>: A calculus for the modeling and simulation of nano devices, Theoretical Computer Science, vol.408, issue.1, pp.17-30, 2008.
DOI : 10.1016/j.tcs.2008.07.006

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Rule-Based Modelling of Cellular Signalling, In CONCUR Lecture Notes in Computer Science, vol.4703, pp.17-41, 2007.
DOI : 10.1007/978-3-540-74407-8_3
URL : https://hal.archives-ouvertes.fr/hal-00164297

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Rule-Based Modelling, Symmetries, Refinements, FMSB, pp.103-122, 2008.
DOI : 10.1007/978-3-540-68413-8_8
URL : https://hal.archives-ouvertes.fr/inria-00528339

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction, 2010 25th Annual IEEE Symposium on Logic in Computer Science, pp.362-381, 2010.
DOI : 10.1109/LICS.2010.44
URL : https://hal.archives-ouvertes.fr/hal-00520112

V. Danos, J. Feret, W. Fontana, and J. Krivine, Abstract Interpretation of Cellular Signalling Networks, VMCAI, pp.83-97, 2008.
DOI : 10.1007/978-3-540-78163-9_11
URL : https://hal.archives-ouvertes.fr/inria-00528352

V. Danos and C. Laneve, Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004.
DOI : 10.1016/j.tcs.2004.03.065
URL : https://hal.archives-ouvertes.fr/hal-00164591

G. Delzanno, C. D. Giusto, M. Gabbrielli, C. Laneve, and G. Zavattaro, The kappa-lattice: Decidability boundaries for qualitative analysis in biological languages, Degano and Gorrieri [15], pp.158-172

J. R. Faeder, M. L. Blinov, and W. S. Hlavacek, Rule-Based Modeling of Biochemical Systems with BioNetGen, Methods in Molecular Biology, vol.500, p.113167, 2009.
DOI : 10.1007/978-1-59745-525-1_5

F. Fages and S. Soliman, Formal Cell Biology in Biocham, In SFM Lecture Notes in Computer Science, vol.5016, pp.54-80, 2008.
DOI : 10.1007/978-3-540-68894-5_3

M. Gibson and J. Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, The Journal of Physical Chemistry A, vol.104, issue.9, pp.1876-1889, 2000.
DOI : 10.1021/jp993732q

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.
DOI : 10.1021/j100540a008

W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka et al., Rules for Modeling Signal-Transduction Systems, Science Signaling, vol.2006, issue.344, p.2006, 2006.
DOI : 10.1126/stke.3442006re6

S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle et al., COPASI--a COmplex PAthway SImulator, Bioinformatics, vol.22, issue.24, pp.223067-3074, 2006.
DOI : 10.1093/bioinformatics/btl485

M. Hucka, A. Finney, H. Sauro, H. Bolouri, J. Doyle et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

M. John, C. Lhoussaine, and J. Niehren, Dynamic compartments in the imperative pi-calculus, Degano and Gorrieri [15], pp.235-250
URL : https://hal.archives-ouvertes.fr/inria-00422970

M. John, C. Lhoussaine, J. Niehren, and A. M. Uhrmacher, The Attributed Pi Calculus, Lecture Notes in Computer Science, vol.5307, pp.83-102, 2008.
DOI : 10.1007/978-3-540-88562-7_10
URL : https://hal.archives-ouvertes.fr/inria-00308970

M. John, C. Lhoussaine, J. Niehren, and C. Versari, Biochemical Reaction Rules with Constraints, Lecture Notes in Computer Science, vol.411, issue.2, pp.338-357, 2011.
DOI : 10.1007/978-3-540-71316-6_28
URL : https://hal.archives-ouvertes.fr/inria-00544387

M. A. Marsan, Stochastic Petri nets: An elementary introduction, European Workshop on Applications and Theory in Petri Nets, pp.1-29, 1988.
DOI : 10.1007/3-540-52494-0_23

R. Meyer, A theory of structural stationarity in the ??-Calculus, Acta Informatica, vol.1, issue.2, pp.87-137, 2009.
DOI : 10.1007/s00236-009-0091-x

R. Meyer and R. Gorrieri, On the Relationship between ??-Calculus and Finite Place/Transition Petri Nets, Lecture Notes in Computer Science, vol.46, issue.2, pp.463-480, 2009.
DOI : 10.1007/3-540-60218-6_4

A. Phillips and L. Cardelli, Efficient, correct simulation of biological processes in the stochastic picalculus, CMSB, pp.184-199, 2007.

C. Priami and P. Quaglia, Beta Binders for Biological Interactions, Danos and Schächter, pp.20-33
DOI : 10.1016/S0020-0190(01)00214-9

A. Regev, E. M. Panina, W. Silverman, L. Cardelli, and E. Y. Shapiro, BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004.
DOI : 10.1016/j.tcs.2004.03.061

M. W. Sneddon, J. R. Faeder, and T. Emonet, Efficient modeling, simulation and coarse-graining of biological complexity with NFsim, Nature Methods, vol.104, issue.2, p.177183, 2011.
DOI : 10.1038/nmeth.1546